* using log directory ‘/data/gannet/ripley/R/packages/tests-devel/rmzqc.Rcheck’
* using R Under development (unstable) (2025-02-15 r87723)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
    GNU Fortran (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
* running under: Fedora Linux 40 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘rmzqc/DESCRIPTION’ ... OK
* this is package ‘rmzqc’ version ‘0.5.4’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘rmzqc’ can be installed ... [12s/16s] OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-gcc/rmzqc-00install.html' for details.
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [10s/13s] OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [8s/11s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [23s/30s] ERROR
  Running ‘testthat.R’ [23s/29s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rmzqc)
  > 
  > test_check("rmzqc")
  Superclass Singleton has cloneable=FALSE, but subclass CV_ has cloneable=TRUE. A subclass cannot be cloneable when its superclass is not cloneable, so cloning will be disabled for CV_.
  trying URL 'https://api.github.com/repos/HUPO-PSI/psi-ms-CV/releases/latest'
  Content type 'application/json; charset=utf-8' length 7324 bytes
  ==================================================
  downloaded 7324 bytes
  
  Downloading obo from 'https://github.com/HUPO-PSI/psi-ms-CV/releases/download/v4.1.191/psi-ms.obo' ...
  trying URL 'https://github.com/HUPO-PSI/psi-ms-CV/releases/download/v4.1.191/psi-ms.obo'
  Content type 'application/octet-stream' length 1008314 bytes (984 KB)
  ==================================================
  downloaded 984 KB
  
  Superclass Singleton has cloneable=FALSE, but subclass CV_ has cloneable=TRUE. A subclass cannot be cloneable when its superclass is not cloneable, so cloning will be disabled for CV_.
  trying URL 'https://api.github.com/repos/HUPO-PSI/psi-ms-CV/releases/latest'
  Content type 'application/json; charset=utf-8' length 7324 bytes
  ==================================================
  downloaded 7324 bytes
  
  Downloading obo from 'https://github.com/HUPO-PSI/psi-ms-CV/releases/download/v4.1.191/psi-ms.obo' ...
  trying URL 'https://github.com/HUPO-PSI/psi-ms-CV/releases/download/v4.1.191/psi-ms.obo'
  Content type 'application/octet-stream' length 1008314 bytes (984 KB)
  ==================================================
  downloaded 984 KB
  
  Downloading obo from 'https://github.com/HUPO-PSI/psi-ms-CV/rele_BROKEN_URL_ases/download/v4.1.147/psi-ms.obo' ...
  trying URL 'https://github.com/HUPO-PSI/psi-ms-CV/rele_BROKEN_URL_ases/download/v4.1.147/psi-ms.obo'
  Error in download.file(custom_uri, tmp_filename) : 
    cannot open URL 'https://github.com/HUPO-PSI/psi-ms-CV/rele_BROKEN_URL_ases/download/v4.1.147/psi-ms.obo'
  Downloading obo from 'https://github.com/HUPO-PSI/psi-ms-CV/rele_BROKEN_URL_ases/download/v4.1.147/psi-ms.obo' ...
  trying URL 'https://github.com/HUPO-PSI/psi-ms-CV/rele_BROKEN_URL_ases/download/v4.1.147/psi-ms.obo'
  Error in download.file(custom_uri, tmp_filename) : 
    cannot open URL 'https://github.com/HUPO-PSI/psi-ms-CV/rele_BROKEN_URL_ases/download/v4.1.147/psi-ms.obo'
  Error in getCVDictionary(source = "custom", custom_uri = "https://github.com/HUPO-PSI/psi-ms-CV/rele_BROKEN_URL_ases/download/v4.1.147/psi-ms.obo",  : 
    Download failed.
  trying URL 'https://api.github.com/repos/HUPO-PSI/psi-ms-CV/releases/latest'
  Content type 'application/json; charset=utf-8' length 7324 bytes
  ==================================================
  downloaded 7324 bytes
  
  Superclass Singleton has cloneable=FALSE, but subclass CV_ has cloneable=TRUE. A subclass cannot be cloneable when its superclass is not cloneable, so cloning will be disabled for CV_.
  Superclass Singleton has cloneable=FALSE, but subclass CV_ has cloneable=TRUE. A subclass cannot be cloneable when its superclass is not cloneable, so cloning will be disabled for CV_.
  Superclass Singleton has cloneable=FALSE, but subclass CV_ has cloneable=TRUE. A subclass cannot be cloneable when its superclass is not cloneable, so cloning will be disabled for CV_.
  Superclass Singleton has cloneable=FALSE, but subclass CV_ has cloneable=TRUE. A subclass cannot be cloneable when its superclass is not cloneable, so cloning will be disabled for CV_.
  Superclass Singleton has cloneable=FALSE, but subclass CV_ has cloneable=TRUE. A subclass cannot be cloneable when its superclass is not cloneable, so cloning will be disabled for CV_.
  [ FAIL 2 | WARN 16 | SKIP 0 | PASS 87 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_conversion.R:17:3'): toQCMetric = function(id, value, on_violation = c("error", "warn")) ──
  `toQCMetric(id = "MS:4000059", value = 13405)` produced messages.
  ── Failure ('test_conversion.R:18:3'): toQCMetric = function(id, value, on_violation = c("error", "warn")) ──
  `toQCMetric(id = "MS:4000059", value = "13405")` produced messages.
  
  [ FAIL 2 | WARN 16 | SKIP 0 | PASS 87 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [49s/62s] OK
* checking PDF version of manual ... [8s/10s] OK
* checking HTML version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 ERROR